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auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

brucezhaor.github.io

:construction: Bruce Zhao's Tech Blog -- Under Reconstructing ...

cellxgene

An interactive explorer for single-cell transcriptomics data

cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

cellxgene_vip

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

excellxgene

genomics

Scripts, utilities and programs for genomic bioinformatics.

hemberg-scrna-seq-course

infercnv

Inferring CNV from Single-Cell RNA-Seq

mast

Tools and methods for analysis of single cell assay data in R

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

sc3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scde

R package for analyzing single-cell RNA-seq data

scnorm

Normalization for single cell RNA-seq data

scpipe

a pipeline for single cell RNA-seq data analysis

scrna-seq-tcc-prep

Preprocessing of single-cell RNA-Seq data for input to kallisto

seurat

R toolkit for single cell genomics

single-cell-3prime-paper

single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

singlecellseq

Batch effects and the effective design of single-cell gene expression studies

splatter

Simple simulation of single-cell RNA sequencing data

zh-google-styleguide

Google 开源项目风格指南 (中文版)